RetrogeneDB ID: retro_amel_1288

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193153.1:840514..840909(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NDUFB7
• Ensembl ID: ENSAMEG00000011470
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa [Source:HGNC Symbol;Acc:7702]

Sequence

>retro_amel_1288
ATGGGAGCGCATCTGGCCTTGTGCTCCCCTGCAAACCGGGGGGGGGGGCTCGACCCCCATGGAATCCCACCTTCTCCCCT
CTTCCCCCACGGCTTCCCGGGGCGCAAGGAGCACGAGAGGGTGGCCACGCAGCCGCAGATGAACGATGTGCAGCTGGTGA
TCCAACAGCGGGAGGACTGCACCCACTAGCTCATCCAGCTGCTCCAGTGCAAGCATGCCAGCTTCCCCAACTTCCTAGCC
TGCGAGCACCAGCAGCACGACAGCGACGACTGCGAGCACGCGGACCACGTGATGCGCAGAAGGCGTCTGAGCAGCAGCAG
GGGCTGCTCCAGGGAAGAAGAGGCAGAAGCAGAAGGAGGCAGATGCGGCCAGAGGCCAAGGGTCCCGGTGAGGTG

Alignment

ORF - retro_amel_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.52 %
• Parental protein coverage: 95.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGAHLARRYVSDPSGEPDPQRMPTFPP-DYGFPGRKEREMVATQQQMSDAQLVLQQRDYCAHYLIRLLKC
          MGAHLA...........DP...P..P....GFPGRKE.E.VATQ.QM.D.QLV.QQR..C.H.LI.LL.C
Retrocopy MGAHLALCSPANXXXXLDPHGIPPSPLFPHGFPGRKEHERVATQPQMNDVQLVIQQREDCTH*LIQLLQC

Parental  KRDSFPNFLACKHEQHDWDYCEHLDYVMR-MKEFERERRLLQ-RKKRREQREAEVARGQ-GPGEV
          K..SFPNFLAC.H.QHD.D.CEH.D.VMR..K..E....LLQ..KKR..Q.EA..ARGQ.GPGEV
Retrocopy KHASFPNFLACEHQQHDSDDCEHADHVMR<QKASEQQQGLLQ<GKKRQKQKEADAARGQ>GPGEV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1288 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011470	1 retrocopy	retro_amel_1288 ,
Canis familiaris	ENSCAFG00000016258	1 retrocopy	retro_cfam_1718,
Dipodomys ordii	ENSDORG00000015213	1 retrocopy	retro_dord_6,
Mus musculus	ENSMUSG00000033938	1 retrocopy	retro_mmus_2539,
Otolemur garnettii	ENSOGAG00000009615	1 retrocopy	retro_ogar_2154,